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<HR>

<H3>3. Basics of using Pizza.py 
</H3>
<P>The <A HREF = "Section_install.txt">previous section</A> describes how to install
and run Pizza.py and the various software it uses.  After Pizza.py has
started you should see a ">" prompt.  The following sections describe
what comes next:
</P>
3.1 <A HREF = "#3_1">Python syntax</A><BR>
3.2 <A HREF = "#3_2">Pizza.py command line arguments</A><BR>
3.3 <A HREF = "#3_3">Pizza.py extensions to the Python interpreter</A><BR>
3.4 <A HREF = "#3_4">Using Pizza.py tools</A><BR>
3.5 <A HREF = "#3_5">Runnning Pizza.py and Python scripts</A><BR>
3.6 <A HREF = "#3_6">Error messages</A> <BR>

<HR>

<H4><A NAME = "3_1"></A>3.1 Python syntax 
</H4>
<P>Aside from its tools, Pizza.py itself simply adds a bit of
functionality to the Python interpreter to enable it to more easily
launch shell commands and scripts and invoke its tools.  Pizza.py's
">" prompt is different from Python's ">>>" prompt to indicate the
extra functionality is available, but you can type any Python command
you would type at the Python prompt.
</P>
<P>Python is a powerful scripting and programming language, similar in
scope and universality to Perl.  This little Pizza.py manual cannot
attempt to teach you how to use Python, its syntax, or its rich set of
powerful built-in commands.  If you only use the extra tools provided
by Pizza.py, you can think of Pizza.py as an application with a
self-contained set of commands.  However, if you learn more about
Python, you will be able to write more powerful Pizza.py scripts,
access and manipulate data stored inside Pizza.py tools, or even add
your own commands and tools, which need not have anything to do with
LAMMPS or ChemCell.
</P>
<P>You can learn about Python at <A HREF = "python">www.python.org</A>.  My most-used
Python book is <A HREF = "http://www.amazon.com/exec/obidos/tg/detail/-/0735709017/104-4868532-2659916?v=glance">Essential Python</A> by Dave Beazley which
assumes some programming experience but covers both the basics of
Python and its many powerful libraries in a well-written, concise
manner.
</P>


<HR>

<H4><A NAME = "3_2"></A>3.2 Pizza.py command line arguments 
</H4>
<P>When running Pizza.py, several command-line options can be added
as switches, e.g.
</P>
<PRE>pizza.py switch args switch args ... 
</PRE>
<DIV ALIGN=center><TABLE  BORDER=1 >
<TR><TD >  -s</TD><TD >	 	              silent (else print start-up help)</TD></TR>
<TR><TD >  -t log dump raster</TD><TD >	      load only these tools</TD></TR>
<TR><TD >  -x raster rasmol</TD><TD >	      load all tools except these</TD></TR>
<TR><TD >  -f file arg1 arg2</TD><TD >          run script file with args</TD></TR>
<TR><TD >  -c "vec = range(100)"</TD><TD >      run Python command</TD></TR>
<TR><TD >  -q</TD><TD > 	   		      quit (else interactive) 
</TD></TR></TABLE></DIV>

<P>Switches can appear in any order and be used multiple times.  The -f
scripts and -c commands are executed in the order they appear.  Script
files are Python files which can contain Python or Pizza.py tool
commands.  Pizza.py looks for script files in 3 places: your current
working directory, the pizza/scripts directory, and any extra
directories you list in the src/DEFAULTS.py file.  This means you can
add your own scripts to pizza/scripts or to directories of your
choosing.
</P>
<P>The argument of the -c switch will typically need to be enclosed in
quotes to avoid being interpreted by the shell.  This also allows
multiple Python commands to be separated by semi-colons, e.g.
</P>
<PRE>-c "a = range(100); print a" 
</PRE>
<HR>

<H4><A NAME = "3_3"></A>3.3 Pizza.py extensions to the Python interpreter 
</H4>
<P>As mentioned above, the standard Python syntax is extended a bit at
the Pizza.py ">" interactive prompt.  These options were inspired by
the <A HREF = "http://www.idyll.org/~n8gray/code/index.html">LazyPython.py</A> code of Nathan Gray, which taught me how to
extend the Python interpreter.  These are the short-cuts:
</P>
<DIV ALIGN=center><TABLE  BORDER=1 >
<TR><TD >  ?</TD><TD >                           print help message</TD></TR>
<TR><TD >  ??</TD><TD >                          one-line for each tool and script</TD></TR>
<TR><TD >  ? raster</TD><TD >                    list tool commands or script syntax</TD></TR>
<TR><TD >  ?? energy.py</TD><TD >                full documentation of tool or script </TD></TR>
<TR><TD >  !ls -l</TD><TD >                      shell command</TD></TR>
<TR><TD >  @cd ..</TD><TD >                      cd to a new directory</TD></TR>
<TR><TD >  @log tmp.log</TD><TD >                log all commands typed so far to file</TD></TR>
<TR><TD >  @run block.py arg1 arg2</TD><TD >     run script file with args</TD></TR>
<TR><TD >  @time d = dump("*.dump")</TD><TD >    time a command 
</TD></TR></TABLE></DIV>



<P>Shell commands begun with a "!" can include the redirection operators
"<" or ">".  The shell command "!cd" will not change directories
permanently; use the "@cd" short-cut instead.  Any short-cut command
starting with "@" can be abbreviated with one or more letters.
E.g. "@r" is the same as "@run".  The @log command requires that the
Python readline library be available on your system.
</P>
<P>Each of the above short-cuts can be performed by native Python
commands; they are just not as simple to type.  Here is how several of
the short-cuts can be written in Python, which is what you need to do
in a script, since the above short-cuts only work at the Pizza.py
interactive prompt:
</P>
<DIV ALIGN=center><TABLE  BORDER=1 >
<TR><TD >Short-cut</TD><TD > Native Python</TD></TR>
<TR><TD >!ls -l</TD><TD > sys.command("ls -l")</TD></TR>
<TR><TD >@cd ..</TD><TD > os.chdir("..")</TD></TR>
<TR><TD >@run myfile.py</TD><TD > execfile("myfile.py")</TD></TR>
<TR><TD >CTRL-D</TD><TD > sys.exit() 
</TD></TR></TABLE></DIV>

<HR>

<H4><A NAME = "3_4"></A>3.4 Using Pizza.py tools 
</H4>
<P>The tools that Pizza.py adds to Python are each implemented as a
single Python class (e.g. dump, log, raster), so the first step in
using a tool is to create an instance of the class (an object).  Each
class defines a set of methods (functions) that operate on the objects
you create and their associated data.  Each method, including the
constructor, takes zero or more arguments, which may be previously
created objects.  In practical terms, this means that you type
commands like this:
</P>
<PRE>d = dump("dump.*")
p = pdb("my.pdb",d)
p.many()
dnew = dump("dump.all") 
</PRE>
<P>The first 2 commands create dump and pdb objects named "d" and "p"
respectively.  The "d" and "p" are Python variable names; you could
use any names you wish: "dump12" or "Dump_mine" or whatever.  The 3rd
line invokes the "many" method within the pdb class for the pdb object
"p".  This method writes out a series of PDB files using the snapshots
in "d" which was passed to "p" when it was created.  The final command
creates a new dump object "dnew" from another dump file.  You can
create and manage as many objects (of the same or different classes)
simultaneously as you wish.  If the last line assigned the object to
"d", the original dump object with the same name would be deleted by
Python.
</P>
<P>Various Pizza.py tools create temporary files as they operate.  These
are all named tmp.*.  Pizza.py does not clean up all of these files,
since they are sometimes useful to look at for debugging or other
purposes.
</P>
<P>Python syntax allows for powerful combinations of tools to be invoked
in one or a few commands.  For example
</P>
<PRE>lg = log("log.*")
m = matlab()
plotview(lg,m) 
</PRE>
<P>could be abbreviated as
</P>
<PRE>plotview(log("log.*"),matlab()) 
</PRE>
<P>With the -c command line switch, this one-liner could be specified
when Pizza.py is launched.  This example also illustrates that created
objects (like the plotview object) do not need to be assigned to
variables if they will not be accessed in subsequent commands.
</P>
<HR>

<H4><A NAME = "3_5"></A>3.5 Running Pizza.py and Python scripts 
</H4>
<P>A file containing Python and/or Pizza.py commands can be executed as a
script and arguments can be passed to it (if desired).  The script can
be run in several different ways:
</P>
<P>(1) From the Pizza.py command line
</P>
<PRE>% pizza -f script.sample file.test 10 ... 
</PRE>
<P>(2) From the Pizza.py interactive prompt
</P>
<PRE>> @run script.sample file.test 10 ... 
</PRE>
<P>(3) From the Python command line
</P>
<PRE>% python -i script.sample file.test 10 ... 
</PRE>
<P>(4) From a shell prompt with #!/usr/local/bin/python -i as 1st line of script
</P>
<PRE>% script.sample arg1 arg2 ... 
</PRE>
<P>(5) From the Python interactive prompt
</P>
<PRE>>>> argv = <B>0,"file.test","10",...</B>
>>> execfile("script.sample") 
</PRE>
<P>(6) As a nested script from within another Python or Pizza.py script file
</P>
<PRE>argv = <B>0,"file.test","10",...</B>
execfile("script.sample") 
</PRE>
<P>The Pizza.py interpreter short-cut commands described
in the next section cannot be used in a script file.
</P>
<P>There are 2 additional issues to address in your script files.
</P>
<P>(A) First, if the script uses Pizza.py commands and you want to run it
from Python itself (methods 3,4,5,6), then your script should import
the necessary Pizza.py tools directly.  E.g. if your script uses the
log and matlab tools, you would put these lines at the top:
</P>
<PRE>from log import log
from matlab import matlab 
</PRE>
<P>This is OK to do even if the script will be run by Pizza.py since it
doesn't matter that Pizza.py already imported the tools.  Note that if
you do this, you can then give your script file and the Python tool
*.py files it uses to someone who doesn't have Pizza.py and they can
run your script with their Python.
</P>
<P>(B) Second, if your script takes arguments and you want the same
script to run identically for all 6 methods, then you need to include
this line at the beginning of the script:
</P>
<PRE>if not globals().has_key("argv"): argv = sys.argv 
</PRE>
<P>This will enable the arguments to be accessed in the script as
argv<B>1</B> for the 1st argument, argv<B>2</B> for the 2nd, etc.
</P>
<P>This works because in methods 3,4 Python stores the script arguments
in sys.argv and the script name in sys.argv<B>0</B>.  The above line of
Python code copies sys.argv to argv.  When Pizza.py runs the script
(methods 1,2) it loads the arguments directly into the "argv"
variable.  Methods 5,6 load the arguments into argv explicitly before
executing the script via execfile().  In this case argv<B>0</B> is a dummy
argument to conform with the Python convention for sys.argv.
</P>
<P>Also note in methods 5,6 that all arguments such as "10" must be
strings even if they are numeric values, since this is the way they
are passed to the script in methods 1,2,3,4.
</P>
<P>As an example of the flexibility enabled by combining scripts,
arguments, and command-line options in Pizza.py, consider the 3-line
example of the previous sub-section.  We modify the script as follows
and save it as logview.py:
</P>
<PRE>files = ' '.join(argv<B>1:</B>)   # create one string from list of filenames
lg = log(files)
m = matlab()
plotview(lg,m) 
</PRE>
<P>If an alias is defined in your shell start-up file, such as
</P>
<PRE>alias logview ~/pizza/src/pizza.py -f logview.py 
</PRE>
<P>then you can type the following one-liner at the shell prompt to
invoke Pizza.py on the logview.py script with a list of files you
specfiy.
</P>
<PRE>% logview log.1 log.2 ... 
</PRE>
<P>A set of plots and a control GUI will appear on your screen.
</P>
<HR>

<H4><A NAME = "3_6"></A>3.6 Error messages 
</H4>
<P>If you mistype a Pizza.py or Python command or pass an invalid
argument to a tool method, an error message will be printed by Python.
Usually these will be self-explanatory.  Sometimes they will point to
a line of code inside a tool which Python was unable to execute
successfully.  This could be because you passed the wrong arguments to
the tool, the data the tool is operating on is invalid, or because
there's a bug in the tool.  In the latter case, please figure out as
much as you can about the bug and email a description and the
necessary files to reproduce the bug in the simplest possible way to
sjplimp@sandia.gov.
</P>
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